The SOFIA Aircraft System (AS) Phase 1 Study was a broad-based study which addressed itself to satisfying technical and programmatic requirements by drawing from existing technology and applying cost-efficient commercial approaches to the aircraft modification. In this SOFIA AS Phase 2 Study, five critical areas of the aircraft were selected for more detailed investigation: forward pressure bulkhead, aft bulkhead, 'free' shell to bulkhead interface, shell cut-out to bulkhead interface, and flooring. The in-depth investigation of these areas upon a finite element model (FEM), with a fine grid model in areas of particular interest, is discussed. The FEM code used is called 'STRAP' and was developed by the engineering firm, Rasmussen and Associates. STRAP is NASTRAN compatible to within 1%. The loads applied to the model were approximated from known 747 envelope conditions. The areas of investigation, and a section through the fuselage is shown. The thrust of this investigation was to develop the design concepts conceived under phase 1 to the point where detailed design could be undertaken with a high level of confidence.